Sat Oct 15 11:53:37 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 11:53:38 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3300 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5742399 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -16.29000 40.06800 ymin,ymax (A): 16.75400 76.39100 zmin,zma (A): 25.04800 87.04300 x,y,z range (A): 56.35800 59.63700 61.99500 scale (grids/A): 0.5742399 object centre (A): 11.88900 46.57250 56.04550 number of atom coordinates read : 3300 total number of charged atoms : 3159 net assigned charge : 13.72602 assigned positive charge : 484.6257 centred at (gu) : 89.94888 90.03333 91.03142 assigned negative charge : -470.9014 centred at (gu) : 89.82943 90.05484 91.21235 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7367 nv = 96 ne = 84 npr = 65230 no. pairs analyzed = 65230 no. exposed pairs = 4366 no. arc points = 31952 no. surface atoms = 1451 nbur = 1849 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 321 mr = 3705 m= 0 mr = 24 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.3900000 number of dielectric boundary points 3959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3171 ## 332 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9327 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6314077E-09 -1.3976589E-09 midg,1,midg; midg,igrid,midg 2.8849432E-09 2.0963433E-09 1,midg,midg; igrid,midg,midg 1.6748430E-10 4.7003321E-09 gauss-seidel spectral radius is 0.9843897 estimated iterations to convergence 66 setup time was (sec) 0.6900000 now iterating at: 11:53:39 rms-change max change #iterations 9.7142816E-02 14.21145 at 10iterations 7.2684810E-03 1.220943 at 20iterations 5.7808816E-04 7.9519510E-02 at 30iterations 5.3280724E-05 7.4996948E-03 at 40iterations 6.9859416E-06 7.3242188E-04 at 50iterations finished qdiffx linear iterations at : 11:53:43 total time elapsed so far: 5.140000 # loops : 50 mean,max change (kT/e) : 6.9859416E-06 7.3242188E-04 energy calculations done at 5.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.300000 DelPhi exited at 11:53:44 5.303u 0.484s 0:06.14 94.1% 0+0k 0+0io 6pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 11:53:44 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3300 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.722720 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -16.29000 40.06800 ymin,ymax (A): 16.75400 76.39100 zmin,zma (A): 25.04800 87.04300 x,y,z range (A): 56.35800 59.63700 61.99500 scale (grids/A): 1.722720 object centre (A): 11.88900 46.57250 56.04550 number of atom coordinates read : 3300 total number of charged atoms : 3159 net assigned charge : 13.72602 assigned positive charge : 484.6257 centred at (gu) : 89.84571 90.09893 93.09316 assigned negative charge : -470.9014 centred at (gu) : 89.48798 90.16415 93.63683 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 80089 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31952 grid for indexing accessible points = 1.400000 m= 25907 mr = 53006 m= 3236 mr = 17928 m= 117 mr = 1736 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 1568 time to turn everything in is 0.7000000 number of dielectric boundary points 36663 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 310 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 24562 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5742399 object centre at (A) : 11.88900 46.57250 56.04550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6952136E-02 1.2276313E-02 midg,1,midg; midg,igrid,midg 3.5513382E-02 1.8810660E-02 1,midg,midg; igrid,midg,midg -6.3355919E-03 1.6616492E-02 gauss-seidel spectral radius is 0.9984249 estimated iterations to convergence 200 setup time was (sec) 1.120000 now iterating at: 11:53:45 rms-change max change #iterations 3.899225 167.6408 at 10iterations 1.711655 56.09015 at 20iterations 0.7549055 26.80644 at 30iterations 0.3334931 10.83788 at 40iterations 0.1471159 4.783295 at 50iterations 6.4702615E-02 2.126446 at 60iterations 2.8806025E-02 0.9307594 at 70iterations 1.2715743E-02 0.4067574 at 80iterations 5.6217820E-03 0.1810913 at 90iterations 2.4910825E-03 7.5084686E-02 at 100iterations 1.0992222E-03 3.4473419E-02 at 110iterations 4.8852467E-04 1.5031815E-02 at 120iterations finished qdiffx linear iterations at : 11:53:57 total time elapsed so far: 12.85000 # loops : 120 mean,max change (kT/e) : 4.8852467E-04 1.5031815E-02 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 11:53:58 13.088u 0.519s 0:14.03 96.8% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 11:53:58 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3300 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.584080 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -16.29000 40.06800 ymin,ymax (A): 16.75400 76.39100 zmin,zma (A): 25.04800 87.04300 x,y,z range (A): 56.35800 59.63700 61.99500 scale (grids/A): 2.584080 object centre (A): 11.88900 46.57250 56.04550 number of atom coordinates read : 3300 total number of charged atoms : 3159 net assigned charge : 13.72602 assigned positive charge : 484.6257 centred at (gu) : 89.76834 90.14828 94.63950 assigned negative charge : -470.9014 centred at (gu) : 89.23184 90.24618 95.45525 start vw surface at 0.1300000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 186102 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31952 grid for indexing accessible points = 1.400000 m= 86848 mr = 130241 m= 27427 mr = 68403 m= 5300 mr = 20910 m= 473 mr = 3621 m= 13 mr = 242 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 5084 time to turn everything in is 1.710000 number of dielectric boundary points 82747 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 25247 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.722720 object centre at (A) : 11.88900 46.57250 56.04550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7135116 0.1305364 midg,1,midg; midg,igrid,midg 0.5486442 0.3446859 1,midg,midg; igrid,midg,midg -4.2356599E-02 0.2226773 gauss-seidel spectral radius is 0.9992262 estimated iterations to convergence 284 setup time was (sec) 2.110000 now iterating at: 11:54:00 rms-change max change #iterations 9.763854 322.0344 at 10iterations 5.690853 146.0192 at 20iterations 3.289225 83.62871 at 30iterations 1.897521 42.92537 at 40iterations 1.087370 22.18791 at 50iterations 0.6228914 13.27453 at 60iterations 0.3542972 7.535568 at 70iterations 0.2023810 3.699680 at 80iterations 0.1150548 2.342220 at 90iterations 6.5500416E-02 1.179162 at 100iterations 3.7197445E-02 0.6911187 at 110iterations 2.1128016E-02 0.4080610 at 120iterations 1.1998131E-02 0.2224274 at 130iterations 6.8018562E-03 0.1218472 at 140iterations 3.8596638E-03 7.1334839E-02 at 150iterations 2.1915587E-03 4.2968750E-02 at 160iterations 1.2432127E-03 2.2786140E-02 at 170iterations 7.0498907E-04 1.2367249E-02 at 180iterations finished qdiffx linear iterations at : 11:54:20 total time elapsed so far: 22.16000 # loops : 180 mean,max change (kT/e) : 7.0498907E-04 1.2367249E-02 energy calculations done at 22.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.33000 DelPhi exited at 11:54:21 22.330u 0.576s 0:23.35 98.0% 0+0k 0+0io 0pf+0w